Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis of the American mink ACE2 binding by Y453F trimeric spike glycoproteins of SARS-CoV-2.
Journal, issue, pages	J Med Virol, Vol. 95, Issue 10, Page e29163, Year 2023
Publish date	Nov 7, 2023
Authors	Hyunjun Ahn / Brenda M Calderon / Xiaoyu Fan / Yunrong Gao / Natalie L Horgan / Nannan Jiang / Dylan S Blohm / Jaber Hossain / Nicole Wedad K Rayyan / Sarah H Osman / Xudong Lin / Michael Currier / John Steel / David E Wentworth / Bin Zhou / Bo Liang /
PubMed Abstract	Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) enters the host cell by binding to angiotensin-converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 receptors differ across ...Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) enters the host cell by binding to angiotensin-converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 receptors differ across various species and differential interactions with Spike (S) glycoproteins of SARS-CoV-2 viruses impact species specificity. Reverse zoonoses led to SARS-CoV-2 outbreaks on multiple American mink (Mustela vison) farms during the pandemic and gave rise to mink-associated S substitutions known for transmissibility between mink and zoonotic transmission to humans. In this study, we used bio-layer interferometry (BLI) to discern the differences in binding affinity between multiple human and mink-derived S glycoproteins of SARS-CoV-2 and their respective ACE2 receptors. Further, we conducted a structural analysis of a mink variant S glycoprotein and American mink ACE2 (mvACE2) using cryo-electron microscopy (cryo-EM), revealing four distinct conformations. We discovered a novel intermediary conformation where the mvACE2 receptor is bound to the receptor-binding domain (RBD) of the S glycoprotein in a "down" position, approximately 34° lower than previously reported "up" RBD. Finally, we compared residue interactions in the S-ACE2 complex interface of S glycoprotein conformations with varying RBD orientations. These findings provide valuable insights into the molecular mechanisms of SARS-CoV-2 entry.
External links	J Med Virol / PubMed:37842796
Methods	EM (single particle)
Resolution	3.36 - 3.87 Å
Structure data	40976 8t20 EMDB-40976, PDB-8t20: Cryo-EM structure of mink variant Y453F trimeric spike protein bound to two mink ACE2 receptors Method: EM (single particle) / Resolution: 3.36 Å 40977 8t21 EMDB-40977, PDB-8t21: Cryo-EM structure of mink variant Y453F trimeric spike protein Method: EM (single particle) / Resolution: 3.6 Å 40978 8t22 EMDB-40978, PDB-8t22: Cryo-EM structure of mink variant Y453F trimeric spike protein bound to one mink ACE2 receptors at downRBD conformation Method: EM (single particle) / Resolution: 3.83 Å 40979 8t23 EMDB-40979, PDB-8t23: Cryo-EM structure of the RBD-ACE2 interface of the SARS-CoV-2 trimeric spike protein bound to ACE2 receptor after local refinement at upRBD conformation Method: EM (single particle) / Resolution: 3.87 Å 40980 8t25 EMDB-40980, PDB-8t25: Cryo-EM structure of the RBD-ACE2 interface of the SARS-CoV-2 trimeric spike protein bound to ACE2 receptor after local refinement at downRBD conformation. Method: EM (single particle) / Resolution: 3.62 Å 41143 8taz EMDB-41143, PDB-8taz: Cryo-EM structure of mink variant Y453F trimeric spike protein bound to one mink ACE2 receptors Method: EM (single particle) / Resolution: 3.75 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose
Source	severe acute respiratory syndrome coronavirus 2 neovison vison (American mink) homo sapiens (human) neogale vison (American mink)
Keywords	VIRAL PROTEIN / Coronavirus / Spike / ACE2 / Mink / Protein binding / SARS-CoV-2